I'm aware that Islam was actually very progressive with regard to women's status in society - the Koran even makes provisions for wives and daughters to inherit and own property, which was basically unheard of back when the Koran was written. Of course, most other non-Muslims are unlikely to know that, so it's a good thing you mentioned it.

Practices such as female genital modification (FGM), "honor killings" and treatment of women as second-class citizens or property are thought by many in the West to be "Muslim" - and I guess they are considered that way by Muslims who do those things. But as you said, they are not really Muslim practices, and in many cases actually contradict what the Koran says about treatment of women.

Those kinds of practices are actually holdovers from traditions that particular peoples practiced before they adopted Islam. It is unfortunate that such abuses of human rights and dignity persisted in spite of Islam and, even worse, that Islam became a justification for/associated with them.